Searching journal content for articles similar to Clark et al. 13 (12): 2747.

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  1. PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
    • Michael R. Brent
    Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
    ...Genome annotation past, present, and future: How to define an ORF at each locus Michael R. Brent Laboratory for Computational Genomics and Department of Computer Science, Washington University, St. Louis, Missouri 63130, USA Abstract Driven by competition...
  2. Methods: Gene and alternative splicing annotation with AIR
    • Liliana Florea,
    • Valentina Di Francesco,
    • Jason Miller,
    • Russell Turner,
    • Alison Yao,
    • Michael Harris,
    • Brian Walenz,
    • Clark Mobarry,
    • Gennady V. Merkulov,
    • Rosane Charlab,
    • Ian Dew,
    • Zuoming Deng,
    • Sorin Istrail,
    • Peter Li,
    • and Granger Sutton
    Genome Res. January 2005 15: 54-66; doi:10.1101/gr.2889405
    ..., at varying degrees of relatedness, we focused on the extended cystic fibrosis transmembrane conductance regulator ( CFTR ) gene region, recently sequenced and comparatively analyzed in 13 species (baboon, cat, chicken, chimp, cow, dog, Fugu , human, mouse, pig, rat, tetraodon, zebrafish) ( Thomas et al. 2003...
  3. ENSEMBL Special: The Ensembl Automatic Gene Annotation System
    • Val Curwen,
    • Eduardo Eyras,
    • T. Daniel Andrews,
    • Laura Clarke,
    • Emmanuel Mongin,
    • Steven M.J. Searle,
    • and Michele Clamp
    Genome Res. May 2004 14: 942-950; doi:10.1101/gr.1858004
    ...the storage and display parts of Ensembl have been used for many s, the automatic annotation has been used for human, mouse, rat, mosquito, Fugu rubripes , zebrafish, and C. briggsae . All these annotations can be found at http://www.ensembl.org . RESULTS AND DISCUSSION In this section we first describe...
  4. LETTER: Genomic Sequence Analysis of Fugu rubripes CFTR and Flanking Genes in a 60 kb Region Conserving Synteny with 800 kb of Human Chromosome 7
    • Heather Davidson,
    • Martin S. Taylor,
    • Ann Doherty,
    • A. Christopher Boyd,
    • and David J. Porteous
    Genome Res. August 1, 2000 10: 1194-1203; doi:10.1101/gr.10.8.1194
    ...in that species in response to salinity may be regulated transcriptionally. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AJ271361 , for the combined cosmids 159C9, 146H13, 6M15, and 145M20.] The puffer fish Fugu rubripes ( Fugu ) has one...
  5. LETTER: Genomic Structure and Comparative Analysis of Nine Fugu Genes: Conservation of Synteny with Human Chromosome Xp22.2–p22.1
    • Bodo Brunner,
    • Tilman Todt,
    • Steffen Lenzner,
    • Karen Stout,
    • Ute Schulz,
    • Hans-Hilger Ropers,
    • and Vera M. Kalscheuer
    Genome Res. May 1, 1999 9: 437-448; doi:10.1101/gr.9.5.437
    ...Homologous to Human Xp22.2–Xp22.1 Initially, three partially overlapping human liver cDNA probes encoding PHKA2 were used to screen a Fugu cosmid library (kindly provided by the Resource Center of the German Human Genome Project). One cosmid, ICRFc66A2095Q1.2 (A2095), was entirely sequenced because it also...
  6. Resource: HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
    • Shengfeng Huang,
    • Zelin Chen,
    • Guangrui Huang,
    • Ting Yu,
    • Ping Yang,
    • Jie Li,
    • Yonggui Fu,
    • Shaochun Yuan,
    • Shangwu Chen,
    • and Anlong Xu
    Genome Res. August 2012 22: 1581-1588; Published in Advance May 3, 2012, doi:10.1101/gr.133652.111
    ..., Christoffels A, Rash S, Hoon S, Smit A, et al. 2002. Whole- shotgun HaploMerger Genome Research 1587 www..org assembly and analysis of the of Fugu rubripes. Science 297: 1301–1310. Barriere A, Yang SP, Pekarek E, Thomas CG, Haag ES, Ruvinsky I. 2009. Detecting heterozygosity in shotgun assemblies: Lessons from...
  7. REVIEW: Cross-Species Sequence Comparisons: A Review of Methods and Available Resources
    • Kelly A. Frazer,
    • Laura Elnitski,
    • Deanna M. Church,
    • Inna Dubchak,
    • and Ross C. Hardison
    Genome Res. January 1, 2003 13: 1-12; doi:10.1101/gr.222003
    ...( Caenorhabditis elegans ), a fruitfly ( Drosophila melanogaster ), thale cress ( Arabidopsis thanliana ), a variety of rice ( Oryza sativa japonica ), a pufferfish ( Fugu ribripes ) and humans ( Homo sapiens ). Other eukaryotic genomic sequences, including those of the mouse and rat, will be completed in the near...
  8. RESOURCE: Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters
    • Albert J. Poustka,
    • Detlef Groth,
    • Steffen Hennig,
    • Sabine Thamm,
    • Andrew Cameron,
    • Alfred Beck,
    • Richard Reinhardt,
    • Ralf Herwig,
    • Georgia Panopoulou,
    • and Hans Lehrach
    Genome Res. December 2003 13: 2736-2746; doi:10.1101/gr.1674103
    ..., and their classification into gene families that include orthologs from protostomes ( Caenorhabditis elegans and Drosophila melanogaster ), deuterostomes ( Ciona intestinalis ), and vertebrates (man, mouse, Fugu ). The role of gene duplications as a major process of increasing the genetic material available to an organism...
  9. PERSPECTIVE: Chicken genome: Current status and future opportunities
    • David W. Burt
    Genome Res. December 2005 15: 1692-1698; doi:10.1101/gr.4141805
    ...: In this window In a new window Table 2. Frequency and class of gene/protein predictions (Ensembl, June 2004) Comparisons between mammals and birds can also start to address questions about gene gains/losses ( Hillier et al. 2004 ). Comparisons between human, chicken, and Fugu suggest a core set of almost one...
  10. LETTER: The mouse genome: Experimental examination of gene predictions and transcriptional start sites
    • Sujit Dike,
    • Vivekanand S. Balija,
    • Lidia U. Nascimento,
    • Zhenyu Xuan,
    • Jacqueline Ou,
    • Theresa Zutavern,
    • Lance E. Palmer,
    • Greg Hannon,
    • Michael Q. Zhang,
    • and W. Richard McCombie
    Genome Res. December 2004 14: 2424-2429; doi:10.1101/gr.3158304
    ...-quarters of all human genes (and by extrapolation, mouse genes) can be recognized in the Fugu ( Aparicio et al. 2002 ). In contrast, only ∼21% of the 58 novel genes detected in this study have identifiable homologs in the sequenced Fugu . This may show circularity in current gene annotation efforts...
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